Noise subtraction using reference channel data has been used to improve signal-to-noise ratio in magnetoencephalography. In this paper, an adaptive noise subtraction model is proposed and parameters for the model are optimized. A criterion to determine an optimal update period for the filter coefficients is proposed based on the ratio of peak amplitude of evoked field (N100m) divided by the output standard deviation. Experiments are carried out using a 40 channel MEG system. From the experiments, the proposed noise subtraction method shows superior performances over existing non-adaptive methods. Two-dimensional topographic map is shown for a diagnosis with a cubic spline interpolation.